Comprehensive Biochemistry Cheat Sheet

Biomolecules and Building Blocks

Carbohydrates

Functions:

• Energy storage
• Structural components
• Cell recognition

Basic unit: Monosaccharides (simple sugars)

Key reactions:

• Glycosidic bond formation: Joins monosaccharides (dehydration synthesis)
• Glycosidic bond hydrolysis: Breaks disaccharides/polysaccharides

Lipids

Characteristics:

• Hydrophobic
• Insoluble in water
• Soluble in organic solvents

Membrane structure:

• Phospholipid bilayer with hydrophilic heads facing outside
• Hydrophobic tails face inward
• Cholesterol regulates membrane fluidity
• Integral and peripheral proteins embedded

Amino Acids and Proteins

Amino acid structure: Central α-carbon bonded to: -NH₂ (amino group), -COOH (carboxyl group), -H, -R (side chain)

Essential amino acids (must obtain from diet): PVT TIM HALL

• Phenylalanine
• Valine
• Threonine
• Tryptophan
• Isoleucine
• Methionine
• Histidine
• Arginine
• Leucine
• Lysine

Amino acid categories:

Protein structure levels:

• Primary: Amino acid sequence
• Secondary: Regular patterns stabilized by H-bonds
  • α-helix: Spiral structure
  • β-sheet: Extended strands
  • Turns and loops
• Tertiary: 3D folding of entire polypeptide chain
  • Stabilized by: Hydrophobic interactions, H-bonds, ionic bonds, disulfide bridges
• Quaternary: Multiple polypeptide subunits arranged together
  • Example: Hemoglobin (2 α and 2 β subunits)

Protein functions:

• Enzymatic catalysis
• Structure and support
• Transport and storage
• Immune protection
• Regulatory (hormones)
• Movement (contractile proteins)
• Signaling

Nucleic Acids

Basic unit: Nucleotide (phosphate + pentose sugar + nitrogenous base)

RNA types:

• mRNA (messenger): Carries genetic information from DNA to ribosome
• tRNA (transfer): Brings amino acids to ribosome during translation
• rRNA (ribosomal): Forms ribosomes, catalyzes peptide bond formation
• snRNA (small nuclear): Involved in RNA processing
• miRNA (micro): Regulates gene expression

Enzymes and Metabolism

Enzyme Basics

Definition: Biological catalysts that increase reaction rates without being consumed Composition: Mostly proteins (some RNA – ribozymes)

Enzyme kinetics:

• Michaelis-Menten equation: v = (Vₘₐₓ × [S]) / (Kₘ + [S])
  • v = reaction velocity
  • Vₘₐₓ = maximum velocity
  • [S] = substrate concentration
  • Kₘ = Michaelis constant (substrate concentration at ½Vₘₐₓ)

Lineweaver-Burk (double-reciprocal) plot:

• 1/v = (Kₘ/Vₘₐₓ)(1/[S]) + 1/Vₘₐₓ
• Y-intercept = 1/Vₘₐₓ
• X-intercept = -1/Kₘ
• Slope = Kₘ/Vₘₐₓ

Enzyme regulation:

Bioenergetics

• First Law of Thermodynamics: Energy can’t be created or destroyed
• Second Law of Thermodynamics: Entropy in the universe increases in spontaneous processes
• Gibbs Free Energy: ΔG = ΔH – TΔS
  • ΔG < 0: Exergonic (spontaneous)
  • ΔG > 0: Endergonic (non-spontaneous)
  • ΔG° = standard free energy change
  • ΔG°’ = standard free energy change at pH 7

Coupled reactions: Unfavorable reactions driven by favorable reactions

• Example: ATP hydrolysis (ΔG°’ = -30.5 kJ/mol) drives endergonic reactions

High-energy compounds:

• ATP (adenosine triphosphate): Primary energy currency
• Phosphoenolpyruvate (PEP): Highest phosphoryl transfer potential
• Creatine phosphate: Energy storage in muscle
• Acetyl-CoA: High-energy thioester bond

Carbohydrate Metabolism

Glycolysis (glucose → pyruvate): Net gain of 2 ATP, 2 NADH

Fate of pyruvate:

• Aerobic: Enters mitochondria, converted to acetyl-CoA
• Anaerobic:
  • Animals: Lactate (NADH regenerated)
  • Yeast/bacteria: Ethanol + CO₂ (NADH regenerated)

Gluconeogenesis (pyruvate → glucose):

• Not simply glycolysis in reverse
• Bypasses irreversible steps of glycolysis
• Key enzymes: Pyruvate carboxylase, PEP carboxykinase, Fructose-1,6-bisphosphatase, Glucose-6-phosphatase
• Energetic cost: 6 ATP equivalents per glucose

Glycogen metabolism:

• Glycogenesis: Glucose → glycogen (storage)
  • Key enzyme: Glycogen synthase
• Glycogenolysis: Glycogen → glucose (mobilization)
  • Key enzyme: Glycogen phosphorylase

Pentose phosphate pathway:

• Functions: NADPH production, ribose-5-phosphate for nucleotide synthesis
• Oxidative phase: G6P → ribulose-5-phosphate + CO₂ (produces NADPH)
• Non-oxidative phase: Interconversion of sugars

Citric Acid Cycle (TCA/Krebs Cycle)

Location: Mitochondrial matrix Net reaction: Acetyl-CoA + 3NAD⁺ + FAD + GDP + Pi + 2H₂O → 2CO₂ + 3NADH + FADH₂ + GTP + 2H⁺ + CoA

Regulation:

• Inhibited by: ATP, NADH
• Key regulatory enzymes: Citrate synthase, Isocitrate dehydrogenase, α-Ketoglutarate dehydrogenase

Electron Transport Chain and Oxidative Phosphorylation

Location: Inner mitochondrial membrane Function: Transfers electrons from NADH/FADH₂ to O₂, coupled to ATP synthesis

Complexes:

• Complex I (NADH dehydrogenase): NADH → FMN → Fe-S → CoQ, pumps 4H⁺
• Complex II (Succinate dehydrogenase): FADH₂ → Fe-S → CoQ, no proton pumping
• Complex III (Cytochrome bc₁): CoQH₂ → Cyt c, pumps 4H⁺
• Complex IV (Cytochrome c oxidase): Cyt c → O₂, pumps 2H⁺

ATP synthase (Complex V):

• Uses proton gradient to synthesize ATP
• F₁ (catalytic) and F₀ (membrane) components
• Approximately 3H⁺ required per ATP synthesized

ATP yield:

• NADH: ~2.5 ATP
• FADH₂: ~1.5 ATP
• Complete glucose oxidation: ~30-32 ATP

Inhibitors:

• Rotenone: Blocks Complex I
• Antimycin A: Blocks Complex III
• Cyanide, carbon monoxide: Block Complex IV
• Oligomycin: Blocks ATP synthase
• Uncouplers (e.g., 2,4-DNP): Dissipate proton gradient without ATP synthesis

Lipid Metabolism

Fatty acid oxidation (β-oxidation):

• Location: Mitochondrial matrix
• Process: Fatty acid activation (uses 2 ATP) → Transport into mitochondria via carnitine shuttle → Repeated cleavage cycles
• Each cycle produces: Acetyl-CoA, NADH, FADH₂
• ATP yield: n/2 acetyl-CoA, n/2-1 NADH, n/2-1 FADH₂ (where n = carbon atoms)
• Example: Palmitate (C16) → 8 acetyl-CoA, 7 NADH, 7 FADH₂ ≈ 106 ATP

Fatty acid synthesis:

• Location: Cytosol
• Starter molecule: Acetyl-CoA (transported from mitochondria as citrate)
• Building blocks: Malonyl-CoA (from acetyl-CoA + CO₂)
• Reducing agent: NADPH (from pentose phosphate pathway)
• Key enzyme: Fatty acid synthase (multi-enzyme complex)
• Process: Repeated cycles of condensation, reduction, dehydration, reduction

Ketone bodies:

• Production (ketogenesis): Liver converts excess acetyl-CoA to acetoacetate, β-hydroxybutyrate, acetone
• Utilization (ketolysis): Tissues convert ketone bodies back to acetyl-CoA
• Significance: Alternative fuel during starvation, diabetes

Cholesterol metabolism:

• Synthesis: Acetyl-CoA → Mevalonate → Squalene → Cholesterol
• Rate-limiting enzyme: HMG-CoA reductase (target of statins)
• Transport: VLDL, LDL (to tissues), HDL (reverse transport)

Amino Acid Metabolism

Transamination: Transfers amino group between amino acids and α-keto acids

• Enzyme: Aminotransferases (transaminases)
• Cofactor: Pyridoxal phosphate (vitamin B₆)

Oxidative deamination: Removes amino group as ammonia

• Key enzyme: Glutamate dehydrogenase
• Products: α-ketoglutarate + NH₄⁺ + NADH

Urea cycle (ammonia detoxification):

• Location: Liver (cytosol and mitochondria)
• Net reaction: 2NH₄⁺ + CO₂ + 3ATP + H₂O → Urea + 2ADP + 2Pi + AMP + PPi
• Steps:
  • Carbamoyl phosphate synthesis (mitochondria)
  • Citrulline formation (mitochondria)
  • Argininosuccinate synthesis (cytosol)
  • Argininosuccinate cleavage → Arginine + Fumarate (cytosol)
  • Arginine hydrolysis → Urea + Ornithine (cytosol)

Amino acid carbon skeleton fates:

• Glucogenic: Converted to glucose precursors (pyruvate, TCA intermediates)
  • Examples: Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Met, Pro, Ser, Thr, Val
• Ketogenic: Converted to acetyl-CoA or acetoacetate
  • Examples: Leu, Lys
• Both glucogenic and ketogenic: Ile, Phe, Trp, Tyr

Molecular Biology and Genetics

DNA Replication

Direction: 5′ → 3′ (DNA polymerase adds nucleotides to 3′ end) Semi-conservative: Each daughter molecule contains one old and one new strand

Key enzymes and proteins:

• Helicase: Unwinds DNA
• Topoisomerase: Relieves supercoiling
• Primase: Synthesizes RNA primers
• DNA polymerase III: Main replicative enzyme
• DNA polymerase I: Removes RNA primers, fills gaps
• Ligase: Seals nicks in DNA
• Single-stranded binding proteins: Stabilize unwound DNA

Replication fork:

• Leading strand: Continuous synthesis
• Lagging strand: Discontinuous synthesis (Okazaki fragments)

Replication initiation:

• Prokaryotes: Single origin of replication (oriC)
• Eukaryotes: Multiple origins

Transcription (DNA → RNA)

Direction: 5′ → 3′ (RNA polymerase adds nucleotides to 3′ end) Template: Antisense (non-coding) DNA strand

Stages:

• Initiation: RNA polymerase binds promoter
• Elongation: Nucleotides added to growing RNA chain
• Termination: RNA release

Prokaryotic vs. Eukaryotic Transcription:

Eukaryotic RNA processing:

• 5′ cap: 7-methylguanosine (protects mRNA, aids translation)
• 3′ poly(A) tail: 100-250 adenine nucleotides (stability, export, translation)
• Splicing: Removal of introns, joining of exons
  • Catalyzed by spliceosome (snRNPs + proteins)
  • Alternative splicing: Different exon combinations

Translation (RNA → Protein)

Direction: N-terminus → C-terminus Location:

• Prokaryotes: Cytoplasm
• Eukaryotes: Cytoplasm (on free or membrane-bound ribosomes)

Genetic code:

• Triplet code: 3 nucleotides (codon) specify 1 amino acid
• Degeneracy: Multiple codons for most amino acids
• Universal: Nearly identical across species
• Start codon: AUG (methionine)
• Stop codons: UAA, UAG, UGA

Components:

• Ribosome: Composed of rRNA and proteins
  • Prokaryotes: 70S (50S + 30S)
  • Eukaryotes: 80S (60S + 40S)
• tRNA: Adapter molecule with anticodon and amino acid attachment site
• Aminoacyl-tRNA synthetases: Attach amino acids to tRNAs

Stages:

• Initiation: Ribosome assembles on mRNA at start codon
• Elongation: Amino acids added sequentially
  • Aminoacyl-tRNA binding
  • Peptide bond formation
  • Translocation
• Termination: Stop codon recognized, protein released

Inhibitors:

• Prokaryotic: Chloramphenicol, tetracycline, erythromycin, streptomycin
• Eukaryotic: Cycloheximide, puromycin
• Both: Puromycin

Gene Regulation

Prokaryotic regulation:

• Operon model: Groups of genes under control of single promoter
• Lac operon (inducible):
  • Repressor: Lac repressor (active without lactose)
  • Inducer: Allolactose (derived from lactose)
  • Positive regulation: CAP-cAMP complex enhances transcription under low glucose
• Trp operon (repressible):
  • Repressor: Trp repressor (active with tryptophan)
  • Corepressor: Tryptophan

Eukaryotic regulation:

Cell Signaling and Membrane Transport

Cell Signaling

Types of signaling:

• Endocrine: Hormones travel via bloodstream
• Paracrine: Local signaling to nearby cells
• Autocrine: Cell signals to itself
• Juxtacrine: Direct cell-cell contact

Signal transduction pathways:

• Receptor activation: Signal binds receptor
• Signal transduction: Cascade of intracellular events
• Cellular response: Gene expression, metabolism, etc.

Major signaling pathways:

Second messengers:

• cAMP: Synthesized by adenylyl cyclase, activates PKA
• cGMP: Synthesized by guanylyl cyclase, activates PKG
• IP₃: Opens Ca²⁺ channels in ER membrane
• DAG: Activates protein kinase C
• Ca²⁺: Binds calmodulin, activates various enzymes

Membrane Transport

Passive transport: No energy required, follows concentration gradient Active transport: Requires energy, can move against concentration gradient

Transport proteins:

Transport mechanisms:

• Simple diffusion: Small, nonpolar molecules through lipid bilayer
• Facilitated diffusion: Specific molecules through channels/carriers
• Primary active transport: Direct ATP hydrolysis
• Secondary active transport:
  • Symport: Both molecules same direction
  • Antiport: Molecules in opposite directions

Bioenergetics and Cellular Respiration Summary

ATP Yield in Cellular Respiration

Complete glucose oxidation:

• Glycolysis: 2 ATP (substrate-level phosphorylation) + 2 NADH (≈ 5 ATP via ETC) = 7 ATP
• Pyruvate dehydrogenase: 2 NADH (≈ 5 ATP)
• TCA cycle: 2 GTP (≈ 2 ATP) + 6 NADH (≈ 15 ATP) + 2 FADH₂ (≈ 3 ATP) = 20 ATP
• Total: Approximately 30-32 ATP

Fatty acid oxidation (palmitate, C16):

• Activation: -2 ATP
• β-oxidation: 7 cycles producing 8 acetyl-CoA, 7 NADH, 7 FADH₂
• Acetyl-CoA oxidation: 8 × 10 ATP = 80 ATP
• NADH: 7 × 2.5 ATP = 17.5 ATP
• FADH₂: 7 × 1.5 ATP = 10.5 ATP
• Total: Approximately 106 ATP

Metabolic Integration

Fed state:

• Glucose: Glycolysis → TCA cycle → ATP production
• Excess glucose: Glycogen synthesis, lipogenesis
• Amino acids: Protein synthesis, some oxidation

Fasting state:

• Glycogen: Glycogenolysis → glucose
• Proteins: Amino acid release → gluconeogenesis
• Triglycerides: Lipolysis → fatty acid oxidation, ketogenesis

Starvation:

• Initial: Similar to fasting
• Prolonged: Ketone bodies as main fuel, protein catabolism decreases
• Terminal: Accelerated protein breakdown

Hormonal regulation:

• Insulin (fed state): Promotes glucose uptake, glycogen synthesis, lipogenesis
• Glucagon (fasting): Stimulates glycogenolysis, gluconeogenesis, lipolysis
• Epinephrine (stress): Similar to glucagon, plus increases heart rate, blood pressure

Common Metabolic Disorders